Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Cola:Echvi_3705 Length = 393 Score = 207 bits (527), Expect = 4e-58 Identities = 137/402 (34%), Positives = 213/402 (52%), Gaps = 22/402 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M E I+S RTP+G ++ G L+ L AI+ A+ RA + P++V++V+MG + Sbjct: 1 MKEVYIISAVRTPLG-SFGGKLSGLTAVELGAQAIKGALGRAQVTPEQVDEVIMGNVLSA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G AR+A + AG+ TT+++ CASG++++ AA+S++ +I V GG ES+ Sbjct: 60 NL-GQAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESM 118 Query: 121 SLVQ--------NDKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170 S V K VD + +VY M + A+ AK ISRE QDEY Sbjct: 119 SNVPYYIPKARFGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTAKEKNISREAQDEY 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 +++S RR A A + F DE+ P++ K + + IT+ +DE + E + Sbjct: 179 AIQSYRRAAEAWKAQAFQDEVIPVTFK---------SRKGESITVDEDEEYQ-NVLFEKI 228 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 L+ V + T+TA NAS ++DGA+A V+MS + A A GL+P+ G +P Sbjct: 229 PSLRPVFDKEGTVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWF 288 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 P A+P+ LK G+ + + +E+NEAF+ L + +L I ++LNV GGA+S+GH Sbjct: 289 TTAPALAIPKALKNAGIQAEAVDYYEINEAFSAVALANQQELNIPNDRLNVFGGAVSLGH 348 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 P G SGAR+ R++ K V +C GGG SA + E Sbjct: 349 PLGASGARIMATLHSVLRQKGGKIGVAGICNGGGGASAMVIE 390 Lambda K H 0.316 0.134 0.378 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 404 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory